The first wooden church on the site was built in 1453 and funded by cardinal Zbigniew Olesnicki's foundation for the reformed branch of the Franciscans called the Bernardines. In the second half of the 15th century a stone building was erected. It was destroyed by the Swedes in 1655. The baroque church that has survived to the present day was built in the years 1659-1676. It was designed by Krzysztof Mieroszewski. It was built in such a way as to keep the line of fire clear for the artillery on the Wawel hill. The church houses paintings of Franciszek Lekszycki, a Bernardine who introduced the techniques of Rubens and van Dyck to polish painting. They are altar paintings, created between the year 1659 and 1664. During the Easter, the Tomb of Jesus is decorated by "Golgota", a painting made by Tadeusz Popiel in 1911, brought to Krakow after the Second World War from Lviv.

In the nothern part of the church lies the chapel of blessed Szymon from Lipnica with the altar-mausoleum made of marble, which houses his relics. The paintings and the stained-glass made by Jozef Mehoffer depict scenes from blessed Szymon's life.